Trying to open .py files on Windows gives cPickle error
Hello,
I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error:
"ModuleNotFoundError: No module named 'cPickle'"
Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible?
Thanks,
Jason
Jason Carnes, PhD Research Scientist IV | Center for Global Infectious Disease Research Seattle Children's Research Institute 206-884-3137 OFFICE
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Hi Jason, Your collaborator is using Chimera, not ChimeraX, and is saving a Chimera session, which ChimeraX cannot read. Either your collaborator needs to start using ChimeraX or you need to use Chimera. Depending on what a "modified file" really means, it may be possible for Chimera to write out other types of files than ChimeraX can read.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 9, 2021, at 4:14 PM, Carnes, Jason via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error:
“ModuleNotFoundError: No module named 'cPickle'”
Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible?
Thanks,
Jason
Jason Carnes, PhD Research Scientist IV | Center for Global Infectious Disease Research Seattle Children's Research Institute 206-884-3137 OFFICE
CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Jason, I am mystified by "their only option to save modified files"... if you mean a modified atomic structure, ChimeraX can write .pdb and .cif (mmCIF), as well as save ChimeraX session files (.cxs). These can be done with the "save" command or menu: File... Save and choosing file type in the dialog.
Maybe that person is using Chimera instead and is saving a Chimera session file (.py) but they would also have the option of writing a PDB file from Chimera, if it is an atomic structure.
In other words, I don't understand why somebody is saying that their only option to save modified files is python, especially if they are really using ChimeraX rather than Chimera! So there shouldn't be any reason why you need to open their python file in ChimeraX. If they are really using Chimera, there is an option to export to ChimeraX that provides a python file, but your opening such a file in ChimeraX should not give that error. As far as I know, this has nothing to do with Mac vs. PC.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2021, at 4:14 PM, Carnes, Jason via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error:
“ModuleNotFoundError: No module named 'cPickle'”
Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible? Thanks, Jason
Elaine,
You are correct that my friend is using Chimera (not ChimeraX). We were a bit confused in our communication on that point.
They can save to a .pdb file, but that file erases all of the color highlighting and hidden parts of the structure that is the reason why we want to share files in the first place.
Can you elaborate on the method to save from Chimera (or export?) in a format that ChimeraX recognizes? I am running ChimeraX and can't see their menu structure.
Thanks so much for your quick reply!!!
Jason
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, August 9, 2021 4:30 PM To: Carnes, Jason Jason.Carnes@seattlechildrens.org Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Trying to open .py files on Windows gives cPickle error
CAUTION: This email originated outside of this organization.
Hi Jason, I am mystified by "their only option to save modified files"... if you mean a modified atomic structure, ChimeraX can write .pdb and .cif (mmCIF), as well as save ChimeraX session files (.cxs). These can be done with the "save" command or menu: File... Save and choosing file type in the dialog.
Maybe that person is using Chimera instead and is saving a Chimera session file (.py) but they would also have the option of writing a PDB file from Chimera, if it is an atomic structure.
In other words, I don't understand why somebody is saying that their only option to save modified files is python, especially if they are really using ChimeraX rather than Chimera! So there shouldn't be any reason why you need to open their python file in ChimeraX. If they are really using Chimera, there is an option to export to ChimeraX that provides a python file, but your opening such a file in ChimeraX should not give that error. As far as I know, this has nothing to do with Mac vs. PC.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2021, at 4:14 PM, Carnes, Jason via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error:
“ModuleNotFoundError: No module named 'cPickle'”
Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible? Thanks, Jason
CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
Hi Jason, Well, the simplest and most foolproof solution if they saved a Chimera session (.py file from Chimera menu:File... Save Session, or Chimera's "save" command) is for you to use Chimera to open it, not ChimeraX!
However, the export to ChimeraX of which I speak is Chimera menu: File... Export Scene, or "export" command. Then they would have to choose or specify the format option : ChimeraX
Here's the Chimera help for Export Scene: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html
If they used this exporting mechanism to save a .py file from Chimera, then you should be able to open it in ChimeraX without error. However, this export does not include every possible thing yet like density maps. If you are working only with atomic structures, however, it may fill the bill.
I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2021, at 5:24 PM, Carnes, Jason via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Elaine,
You are correct that my friend is using Chimera (not ChimeraX). We were a bit confused in our communication on that point.
They can save to a .pdb file, but that file erases all of the color highlighting and hidden parts of the structure that is the reason why we want to share files in the first place.
Can you elaborate on the method to save from Chimera (or export?) in a format that ChimeraX recognizes? I am running ChimeraX and can't see their menu structure.
Thanks so much for your quick reply!!!
Jason
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, August 9, 2021 4:30 PM To: Carnes, Jason Jason.Carnes@seattlechildrens.org Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Trying to open .py files on Windows gives cPickle error
CAUTION: This email originated outside of this organization.
Hi Jason, I am mystified by "their only option to save modified files"... if you mean a modified atomic structure, ChimeraX can write .pdb and .cif (mmCIF), as well as save ChimeraX session files (.cxs). These can be done with the "save" command or menu: File... Save and choosing file type in the dialog.
Maybe that person is using Chimera instead and is saving a Chimera session file (.py) but they would also have the option of writing a PDB file from Chimera, if it is an atomic structure.
In other words, I don't understand why somebody is saying that their only option to save modified files is python, especially if they are really using ChimeraX rather than Chimera! So there shouldn't be any reason why you need to open their python file in ChimeraX. If they are really using Chimera, there is an option to export to ChimeraX that provides a python file, but your opening such a file in ChimeraX should not give that error. As far as I know, this has nothing to do with Mac vs. PC.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2021, at 4:14 PM, Carnes, Jason via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error:
“ModuleNotFoundError: No module named 'cPickle'”
Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible? Thanks, Jason
CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Elaine,
Thank you so much for that Chimera export help! That has solved the problem entirely. I truly appreciate you taking the time to guide us through it.
Cheers,
Jason
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, August 9, 2021 5:32 PM To: Carnes, Jason Jason.Carnes@seattlechildrens.org Cc: ChimeraX Users Help ChimeraX-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Trying to open .py files on Windows gives cPickle error
CAUTION: This email originated outside of this organization.
Hi Jason, Well, the simplest and most foolproof solution if they saved a Chimera session (.py file from Chimera menu:File... Save Session, or Chimera's "save" command) is for you to use Chimera to open it, not ChimeraX!
However, the export to ChimeraX of which I speak is Chimera menu: File... Export Scene, or "export" command. Then they would have to choose or specify the format option : ChimeraX
Here's the Chimera help for Export Scene: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuid... >
If they used this exporting mechanism to save a .py file from Chimera, then you should be able to open it in ChimeraX without error. However, this export does not include every possible thing yet like density maps. If you are working only with atomic structures, however, it may fill the bill.
I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2021, at 5:24 PM, Carnes, Jason via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Elaine,
You are correct that my friend is using Chimera (not ChimeraX). We were a bit confused in our communication on that point.
They can save to a .pdb file, but that file erases all of the color highlighting and hidden parts of the structure that is the reason why we want to share files in the first place.
Can you elaborate on the method to save from Chimera (or export?) in a format that ChimeraX recognizes? I am running ChimeraX and can't see their menu structure.
Thanks so much for your quick reply!!!
Jason
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, August 9, 2021 4:30 PM To: Carnes, Jason Jason.Carnes@seattlechildrens.org Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Trying to open .py files on Windows gives cPickle error
CAUTION: This email originated outside of this organization.
Hi Jason, I am mystified by "their only option to save modified files"... if you mean a modified atomic structure, ChimeraX can write .pdb and .cif (mmCIF), as well as save ChimeraX session files (.cxs). These can be done with the "save" command or menu: File... Save and choosing file type in the dialog.
Maybe that person is using Chimera instead and is saving a Chimera session file (.py) but they would also have the option of writing a PDB file from Chimera, if it is an atomic structure.
In other words, I don't understand why somebody is saying that their only option to save modified files is python, especially if they are really using ChimeraX rather than Chimera! So there shouldn't be any reason why you need to open their python file in ChimeraX. If they are really using Chimera, there is an option to export to ChimeraX that provides a python file, but your opening such a file in ChimeraX should not give that error. As far as I know, this has nothing to do with Mac vs. PC.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2021, at 4:14 PM, Carnes, Jason via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error:
“ModuleNotFoundError: No module named 'cPickle'”
Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible? Thanks, Jason
CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinf o/chimerax-users__;!!NuzbfyPwt6ZyPHQ!5sncYicZMg-r5mtKFMvHWYv1w_ZWXe4LM mopGUXCdHrrn1N7dnBxsRHsGhuWR8alHEHV6xTJ-Q$
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Great!!! I'm glad it worked for your data!
Nowadays I'd rather work with ChimeraX than Chimera, so I've used the export a few times myself...
Best, Elaine
On Aug 9, 2021, at 5:55 PM, Carnes, Jason via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Elaine,
Thank you so much for that Chimera export help! That has solved the problem entirely. I truly appreciate you taking the time to guide us through it.
Cheers,
Jason
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, August 9, 2021 5:32 PM To: Carnes, Jason Jason.Carnes@seattlechildrens.org Cc: ChimeraX Users Help ChimeraX-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Trying to open .py files on Windows gives cPickle error
CAUTION: This email originated outside of this organization.
Hi Jason, Well, the simplest and most foolproof solution if they saved a Chimera session (.py file from Chimera menu:File... Save Session, or Chimera's "save" command) is for you to use Chimera to open it, not ChimeraX!
However, the export to ChimeraX of which I speak is Chimera menu: File... Export Scene, or "export" command. Then they would have to choose or specify the format option : ChimeraX
Here's the Chimera help for Export Scene: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuid... >
If they used this exporting mechanism to save a .py file from Chimera, then you should be able to open it in ChimeraX without error. However, this export does not include every possible thing yet like density maps. If you are working only with atomic structures, however, it may fill the bill.
I hope this helps,
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2021, at 5:24 PM, Carnes, Jason via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Elaine,
You are correct that my friend is using Chimera (not ChimeraX). We were a bit confused in our communication on that point.
They can save to a .pdb file, but that file erases all of the color highlighting and hidden parts of the structure that is the reason why we want to share files in the first place.
Can you elaborate on the method to save from Chimera (or export?) in a format that ChimeraX recognizes? I am running ChimeraX and can't see their menu structure.
Thanks so much for your quick reply!!!
Jason
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, August 9, 2021 4:30 PM To: Carnes, Jason Jason.Carnes@seattlechildrens.org Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Trying to open .py files on Windows gives cPickle error
CAUTION: This email originated outside of this organization.
Hi Jason, I am mystified by "their only option to save modified files"... if you mean a modified atomic structure, ChimeraX can write .pdb and .cif (mmCIF), as well as save ChimeraX session files (.cxs). These can be done with the "save" command or menu: File... Save and choosing file type in the dialog.
Maybe that person is using Chimera instead and is saving a Chimera session file (.py) but they would also have the option of writing a PDB file from Chimera, if it is an atomic structure.
In other words, I don't understand why somebody is saying that their only option to save modified files is python, especially if they are really using ChimeraX rather than Chimera! So there shouldn't be any reason why you need to open their python file in ChimeraX. If they are really using Chimera, there is an option to export to ChimeraX that provides a python file, but your opening such a file in ChimeraX should not give that error. As far as I know, this has nothing to do with Mac vs. PC.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2021, at 4:14 PM, Carnes, Jason via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error:
“ModuleNotFoundError: No module named 'cPickle'”
Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible? Thanks, Jason
CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinf o/chimerax-users__;!!NuzbfyPwt6ZyPHQ!5sncYicZMg-r5mtKFMvHWYv1w_ZWXe4LM mopGUXCdHrrn1N7dnBxsRHsGhuWR8alHEHV6xTJ-Q$
CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
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participants (3)
-
Carnes, Jason -
Elaine Meng -
Eric Pettersen